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Individual miRNAs may regulate hundreds of genes, giving rise to a complex gene regulatory network in which transcripts carrying miRNA binding sites act as competing endogenous RNAs (ceRNAs). Several methods for the analysis of ceRNA interactions exist, but these do often not adjust for statistical confounders or address the problem that more than one miRNA interacts with a target transcript.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present SPONGE, a method for the fast construction of ceRNA networks. SPONGE uses \u2019multiple sensitivity correlation\u2019, a newly defined measure for which we can estimate a distribution under a null hypothesis. SPONGE can accurately quantify the contribution of multiple miRNAs to a ceRNA interaction with a probabilistic model that addresses previously neglected confounding factors and allows fast P-value calculation, thus outperforming existing approaches. We applied SPONGE to paired miRNA and gene expression data from The Cancer Genome Atlas for studying global effects of miRNA-mediated cross-talk. Our results highlight already established and novel protein-coding and non-coding ceRNAs which could serve as biomarkers in cancer.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>SPONGE is available as an R\/Bioconductor package (doi: 10.18129\/B9.bioc.SPONGE).<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz314","type":"journal-article","created":{"date-parts":[[2019,4,26]],"date-time":"2019-04-26T11:28:33Z","timestamp":1556278113000},"page":"i596-i604","source":"Crossref","is-referenced-by-count":46,"title":["Large-scale inference of competing endogenous RNA networks with sparse partial correlation"],"prefix":"10.1093","volume":"35","author":[{"given":"Markus","family":"List","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbr\u00fccken, Germany"},{"name":"Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azim","family":"Dehghani Amirabad","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbr\u00fccken, Germany"},{"name":"Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarbr\u00fccken, Germany"},{"name":"Graduate School of Computer Science, Saarland Informatics Campus, Saarland University, Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Kostka","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology, Department of Computational & Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcel H","family":"Schulz","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbr\u00fccken, Germany"},{"name":"Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarbr\u00fccken, Germany"},{"name":"Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany"},{"name":"German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany (MHS)"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,7,5]]},"reference":[{"key":"2023062712423895300_btz314-B1","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"eLife"},{"key":"2023062712423895300_btz314-B2","doi-asserted-by":"crossref","first-page":"363.","DOI":"10.1038\/msb.2010.24","article-title":"Target mRNA abundance dilutes microRNA and siRNA activity","volume":"6","author":"Arvey","year":"2010","journal-title":"Mol. 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